Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
diff varscan_mpileup2snp.xml @ 1:9a39c4105901 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
| author | erasmus-medical-center |
|---|---|
| date | Wed, 15 Feb 2017 16:16:01 -0500 |
| parents | 0c5cc5763091 |
| children |
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--- a/varscan_mpileup2snp.xml Thu Nov 05 09:59:46 2015 -0500 +++ b/varscan_mpileup2snp.xml Wed Feb 15 16:16:01 2017 -0500 @@ -1,38 +1,35 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from a mpileup file" version="2.3.6.a"> +<tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from a mpileup file" version="2.4.2.a"> <description>VarScan2 SNP/SNV detection; directly from a *.mpileup file.</description> <requirements> - <requirement type="package" version="2.3.6">varscan</requirement> + <requirement type="package" version="2.4.2">varscan</requirement> </requirements> - <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> + <version_command>varscan 2>&1 | head -n 1</version_command> - <command> - cat $mpileup_input | java - -Xmx64G - -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar - mpileup2snp - - #if $extended_parameters.parameters == "extended" - --min-coverage $extended_parameters.varscan_min_coverage - --min-reads2 $extended_parameters.varscan_min_reads2 - --min-avg-qual $extended_parameters.varscan_min_avg_qual - --min-var-freq $extended_parameters.varscan_min_var_freq - --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom - --p-value $extended_parameters.varscan_p_value - $extended_parameters.varscan_strand_filter - $extended_parameters.varscan_variants - #end if - - #if $varscan_output == "vcf" or $varscan_output.value == "vcf" - --output-vcf 1 - #end if - - 2> stderr.txt - > $snv_output ; - cat stderr.txt - </command> + <command detect_errors="exit_code"><![CDATA[ + varscan mpileup2snp + + '${mpileup_input}' + + #if $extended_parameters.parameters == "extended" + --min-coverage $extended_parameters.varscan_min_coverage + --min-reads2 $extended_parameters.varscan_min_reads2 + --min-avg-qual $extended_parameters.varscan_min_avg_qual + --min-var-freq $extended_parameters.varscan_min_var_freq + --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom + --p-value $extended_parameters.varscan_p_value + $extended_parameters.varscan_strand_filter + $extended_parameters.varscan_variants + #end if + + #if $varscan_output == "vcf" or $varscan_output.value == "vcf" + --output-vcf 1 + #end if + + > '${snv_output}' + ]]></command> <inputs> <param format="pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/><!-- datatype "mpileup" does not exist.. it seems to be common to use pileup instead? --> @@ -78,10 +75,27 @@ <output name="snv_output" file="hg19_mutant.vcf" /> </test> + <test> + <param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="pileup" /> + <param name="parameters" value="extended" /> + + <param name="varscan_min_coverage" value="8" /> + <param name="varscan_min_reads2" value="2" /> + <param name="varscan_min_avg_qual" value="15" /> + <param name="varscan_min_var_freq" value="0.01" /> + <param name="varscan_min_freq_for_hom" value="0.75" /> + <param name="varscan_p_value" value="0.99" /> + <param name="varscan_strand_filter" value=" --strand_filter 1" /> + <param name="varscan_variants" value=" --variants 0" /> + + <param name="varscan_output_vcf" value="1" /> + + <output name="snv_output" file="hg19_mutant.2.vcf" /> + </test> </tests> <help> -**VarScan 2.3.6** +**VarScan 2.4.2** VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. http://dx.doi.org/10.1101/gr.129684.111 @@ -92,42 +106,14 @@ Other people were aware of this and have written a version that can do parallelization: https://github.com/mydatascience/parallel-mpileup -Consequently, when a BAM files gets processed by this wrapper, it's processed by *parallel-mpileup* before its send to VarScan. - .. _VarScan: http://varscan.sourceforge.net/ **Input formats** VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing. -**Installation** - -Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment. - -**License** - -* VarScan2.3.6: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0) -* parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING) - -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.dtls.nl/ - -http://toolshed.g2.bx.psu.edu/ - -http://testtoolshed.g2.bx.psu.edu/ </help> <citations> <citation type="doi">10.1101/gr.129684.111</citation> </citations> -</tool> \ No newline at end of file +</tool>